Human Gene CXCL13 (ENST00000682537.1_2) from GENCODE V47lift37
  Description: C-X-C motif chemokine ligand 13, transcript variant 2 (from RefSeq NM_001371558.1)
Gencode Transcript: ENST00000682537.1_2
Gencode Gene: ENSG00000156234.8_6
Transcript (Including UTRs)
   Position: hg19 chr4:78,526,974-78,532,988 Size: 6,015 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr4:78,527,020-78,532,193 Size: 5,174 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:78,526,974-78,532,988)mRNA (may differ from genome)Protein (109 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CXCL13
Diseases sorted by gene-association score: angioimmunoblastic t-cell lymphoma (7), burkitt lymphoma (7), lymphoma (6), asymptomatic neurosyphilis (5), sjogren's syndrome (5), neurosyphilis (3), lymphoma, malt, somatic (2), thymic hyperplasia (2), pleural disease (2), multiple sclerosis, disease progression, modifier of (1), tertiary neurosyphilis (1), acute salpingitis (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -12.8046-0.278 Picture PostScript Text
3' UTR -169.10795-0.213 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001089 - Chemokine_CXC
IPR018048 - Chemokine_CXC_CS
IPR002473 - Chemokine_CXCL8/IL8
IPR001811 - Chemokine_IL8-like_dom

Pfam Domains:
PF00048 - Small cytokines (intecrine/chemokine), interleukin-8 like

SCOP Domains:
54117 - Interleukin 8-like chemokines

ModBase Predicted Comparative 3D Structure on Q53X90
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0008009 chemokine activity

Biological Process:
GO:0006935 chemotaxis
GO:0006952 defense response
GO:0006955 immune response
GO:0010469 regulation of receptor activity
GO:0060326 cell chemotaxis

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space


-  Descriptions from all associated GenBank mRNAs
  AF044197 - Homo sapiens B lymphocyte chemoattractant BLC mRNA, complete cds.
LP880250 - Sequence 54 from Patent WO2017181111.
LP882079 - Sequence 21 from Patent WO2017181079.
MB143800 - JP 2019515670-A/11: METHODS FOR MONITORING AND TREATING CANCER.
MB423124 - JP 2019521641-A/11: METHODS FOR MONITORING AND TREATING CANCER.
BC012589 - Homo sapiens chemokine (C-X-C motif) ligand 13, mRNA (cDNA clone MGC:13521 IMAGE:4246053), complete cds.
JD248257 - Sequence 229281 from Patent EP1572962.
JD368604 - Sequence 349628 from Patent EP1572962.
AF029894 - Homo sapiens Angie mRNA, complete cds.
AJ002211 - Homo sapiens cDNA for a CXC chemokine.
KJ893077 - Synthetic construct Homo sapiens clone ccsbBroadEn_02471 CXCL13 gene, encodes complete protein.
AB590683 - Synthetic construct DNA, clone: pFN21AE1605, Homo sapiens CXCL13 gene for chemokine (C-X-C motif) ligand 13, without stop codon, in Flexi system.
CR407624 - Homo sapiens full open reading frame cDNA clone RZPDo834C102D for gene CXCL13, chemokine (C-X-C motif) ligand 13 (B-cell chemoattractant) complete cds, without stopcodon.
HQ448702 - Synthetic construct Homo sapiens clone IMAGE:100072146; CCSB006321_02 chemokine (C-X-C motif) ligand 13 (B-cell chemoattractant) (CXCL13) gene, encodes complete protein.
JD516577 - Sequence 497601 from Patent EP1572962.
JD552571 - Sequence 533595 from Patent EP1572962.
JD347823 - Sequence 328847 from Patent EP1572962.
JD204375 - Sequence 185399 from Patent EP1572962.
JD284689 - Sequence 265713 from Patent EP1572962.
JD436508 - Sequence 417532 from Patent EP1572962.
JD332108 - Sequence 313132 from Patent EP1572962.
JD510471 - Sequence 491495 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A0A024RDB7, CXCL13 , hCG_22991 , NM_001371558, Q53X90, Q53X90_HUMAN, uc330kbj.1, uc330kbj.2
UCSC ID: ENST00000682537.1_2
RefSeq Accession: NM_001371558.1
Protein: Q53X90

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.